Ionization-loss stimulated Raman spectroscopy for conformational probing of flexible molecules

The approach of studying structural and dynamical properties of flexible molecules is of substantial interest, as it allows decoding the shapes and intrinsic properties of isolated molecular constituents, which have an influence on the selectivity and functionality in biological processes. Combining quantum computation methods with double resonance or infrared hole burning techniques, mainly covering hydride stretch vibrations, recently led to great progress in understanding the structure of a variety of biological building blocks. Measurements of spectra in the lower frequency range, with relatively compact and convenient laser sources, still pose major challenges. For this reason, the method of ionization-loss stimulated Raman spectroscopy (ILSRS) has been developed and applied for monitoring the spectral features of the 2-phenylethanol prototype. The bands observed in the Raman spectra of its two conformers uniquely identify their structures and are in accord with anharmonic results obtained by density functional theory calculations. These findings point to future opportunities for ILSRS as a powerful conformational probe and set new standards for detailed interrogation of structure and intra- and inter-molecular interactions.     

Characterization of thalidomide using Raman spectroscopy

Thalidomide is a potent anticancer therapeutic drug whose mechanism of action has not yet been elucidated. In this report, experimental Raman spectroscopy is used to determine and characterize the vibrational frequencies of the drug. These normal modes are then compared to their quantum mechanical counterparts, which have been computed using density functional theory. Upon analysis of the spectra, we found that there was a high level of agreement between the wavenumbers. As such, this spectroscopic technique may be a viable tool for examining the way in which this drug interacts with its target molecules.     

Raman spectroscopy of octadecylsilane stationary phase conformational order. Effect of solvent

The effect of solvent on the conformation of alkyl chains of two octadecysilane-based stationary phases is probed using Raman spectroscopy. Spectral data indicate that the alkyl chains of commercially available polymeric and monomeric solid-phase extraction stationary phases are disordered to a varying extent by solvents of different polarity. For the polymeric octadecylsilane stationary phase, the polar solvents water, acetonitrile, methanol, acetone and isopropanol have little impact on the conformational order of the octadecylsilane bonded phase relative to air. However, the alkyl portion of this stationary phase is substantially disordered in the low-polarity solvents tetrahydrofuran, chloroform, benzene, toluene and hexane. The monomeric octadecylsilane stationary phase is less susceptible to disordering by solvents, although more disorder in the less polar solvents is also observed for this system. These results are interpreted in terms of the local surface bonding density and interchain spacing of these two stationary phases, and the ability of the solvent to penetrate the chains as a function of polarity. The results clearly demonstrate the ability of Raman spectroscopy to precisely indicate subtle changes in conformational order of alkylsilane stationary phases.     

Polymer crystallinity studied using Raman spectroscopy

The application of Raman spectroscopy to the study of crystallinity in polymers has been examined. In particular, Fourier transform (FT)-Raman spectroscopy has been applied in a number of studies in recent years to investigate crystallinity in a variety of polymers. The polymers discussed in this review are polyethylene, polystyrene, poly(ether ether ketone), polyamides, poly(ethylene terephthalate), elastomers, liquid crystalline polymers, inorganic polymers and certain polymer blends.     

Characterization of amino acids using Raman spectroscopy

A key process in the development of new drugs is elucidation of the interaction between the drug molecule and the target protein. Such knowledge then makes it possible to make systematic structural modifications of the drug molecule to optimize the interaction. Many analytical techniques can be applied to proteins in solution such as circular dichroism, ultraviolet, and fluorescence spectroscopy but these all have limitations. In this paper, we investigate the feasibility of using relatively simple, visible light Raman spectroscopic methods to investigate amino acids and related biopolymers.     

Rapid monitoring of antibiotics using Raman and surface enhanced Raman spectroscopy

Comparatively few studies have explored the ability of Raman spectroscopy for the quantitative analysis of microbial secondary metabolites in fermentation broths. In this study we investigated the ability of Raman spectroscopy to differentiate between different penicillins and to quantify the level of penicillin in fermentation broths. However, the Raman signal is rather weak, therefore the Raman signal was enhanced using surface enhanced Raman spectroscopy (SERS) employing silver colloids. It was difficult by eye to differentiate between the five different penicillin molecules studied using Raman and SERS spectra, therefore the spectra were analysed by multivariate cluster analysis. Principal components analysis (PCA) clearly showed that SERS rather than the Raman spectra produced reproducible enough spectra to allow for the recovery of each of the different penicillins into their respective five groups. To highlight this further the first five principal components were used to construct a dendrogram using agglomerative clustering, and this again clearly showed that SERS can be used to identify which penicillin molecule was being analysed, despite their molecular similarities. With respect to the quantification of penicillin G it was shown that Raman spectroscopy could be used to quantify the amount of penicillin present in solution when relatively high levels of penicillin were analysed (>50 mM). By contrast, the SERS spectra showed reduced fluorescence, and improved signal to noise ratios from considerably lower concentrations of the antibiotic. This could prove to be advantageous in industry for monitoring low levels of penicillin in the early stages of antibiotic production. In addition, SERS may have advantages for quantifying low levels of high value, low yield, secondary metabolites in microbial processes.     

Fast Raman spectroscopy of cytochrome c using intracavity resonance Raman amplification

The resonance Raman spectrum of cytochrome c (5 × 10^?4 M) was obtained using the method of resonance Raman amplification (RRA) in a dye laser resonator in 30 ns. The second harmonic of a Q-switched Nd glass laser was used as an excitation source and the spectra were recorded using a photographic plate.     

Raman amplification spectroscopy using pulsed dye lasers

A picosecond laser system consisting of a mode-locked argon-ion laser synchronously pumping two dye lasers is used for studies of Raman amplification spectra. The two dye laser beams, one kept constant in frequency while the other is tunable, coincide in the Raman sample. Recording the gain or the loss in intensity of one of the lasers as a function of frequency difference produces the Raman spectrum. Good signal to noise ratios have been obtained for a variety of liquids and solids. Fluorescing samples can be studied in the Inverse Raman method where the loss on the higher frequency laser is monitored.     

Determination of conformational preferences of dipeptides using vibrational spectroscopy

The NMR coupling constants ((3)J(H(N), H(alpha))) of dipeptides indicate that the backbone conformational preferences vary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denatured proteins, and the coil regions of native proteins. Detailed characterization of the conformational preferences of dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here, we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. The main advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, which enables the determination of the conformational preferences of short-lived states. Accuracy of structure determination using vibrational spectroscopy depends critically on identification of the vibrational parameters that are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the (3)J(H(N), H(alpha)). These two infrared vibrational parameters are thus analogous to (3)J(H(N), H(alpha)), indicators for the preference for the dihedral angle phi. We also show that the intensities of the components of the amide III bands in infrared spectra and the intensities of the skeletal vibrations in Raman spectra are indicators of populations of the P(II), beta, and alpha(R) conformations. The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the beta conformation increases in valine dipeptides. The populations of the alpha(R) conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.     

Detection of the site of phosphorylation in a peptide using Raman spectroscopy and partial least squares discriminant analysis

Normal (non-enhanced) Raman spectroscopy is used to determine the site of phosphorylation on a 13-residue peptide whose sequence derives from the cellular protein pp60(c-src) (protein tyrosine kinase). Raman spectra of serine, threonine and tyrosine amino acids and their phosphorylated derivatives are used to aid in the interpretation of peptide spectra. The purity of the synthetic peptides are confirmed by mass spectroscopy. Peptide Raman measurements are performed using the recently reported drop-coating deposition Raman (DCDR) method, followed by Savistky-Golay second derivative (SGSD) pre-processing and multivariate spectral classification using partial least squares (PLS) discriminant analysis. Leave-one-out training/testing results are displayed using a PLS psuedo-probability score plot and shown to facilitate error-free spectral determination of the site of phosphorylation.     

Investigating microcrystalline cellulose crystallinity using Raman spectroscopy

Cellulose - Microcrystalline cellulose (MCC) is a semi-crystalline material with inherent variable crystallinity due to raw material source and variable manufacturing conditions. MCC crystallinity...     

A Rheumatoid arthritis study using Raman spectroscopy

Rheumatoid arthritis (RA) is characterized by chronic inflammation of the joints and can lead to a progressive destruction of articular cartilage and bone. In this study, the specificity and sensitivity of the RA diagnostic methods based on the receiver-operating characteristic curves for monitoring C-reactive protein (CRP) and rheumatoid factor (RF) were compared with the Raman spectroscopic diagnostic method developed in this work. Sera from 24 patients with rheumatoid arthritis and from 16 healthy individuals were analyzed to assess the biochemical composition and presence of inflammatory activity by the aforementioned methods. By comparing with the clinical results for specificity and sensitivity from the RF and CRP tests, we show that the overall results from the newly developed Raman method were significantly better, with a specificity of 96%, a sensitivity of 88%, and correctly identifying 92% of the RA and healthy individuals, while the RF test gave a specificity of 100% and a sensitivity of 54%, and the CRP test gave a specificity of 87% and a sensitivity of 58%, respectively.     

Towards single-microorganism detection using surface-enhanced Raman spectroscopy

The identification and discrimination of microorganisms is important not only for clinical reasons but also for pharmaceutical clean room production and food-processing technology. Vibrational spectroscopy such as IR, Raman, and surface-enhanced Raman scattering (SERS) can provide a rapid ‘fingerprint’ on the chemical structure of molecules and is used to obtain a ‘fingerprint’ from microorganisms as well. Because of the requirement that a single bacterium cell and noble metal nanoparticles must be in close contact and the lack of a significant physical support to hold nanoparticles around the single bacterium cell, the acquisition of SERS spectra for a single bacterium using colloidal nanoparticles could be a challenging task. The feasibility of SERS for identification down to a single bacterium is investigated. A Gram-negative bacterium, Escherichia coli, is chosen as a model for the investigation. Because the adsorption of silver nanoparticles onto the bacterial cell is an exclusive way for locating nanoparticles close to the bacterium cell, the absorption characteristics of silver nanoparticles with different surface charges are investigated. It is demonstrated that the citrate-reduced colloidal silver solution generates more reproducible SERS spectra. It is found that E. coli cells aggregate upon mixing with silver colloidal solution, and this may provide an additional benefit in locating the bacterial cell under a light microscope. It is also found that a laser wavelength in the UV region could be a better choice for the study due to the shallow penetration depth. It is finally shown that it is possible to obtain SERS spectra from a single cell down to a few bacterial cells, depending on the aggregation properties of bacterial cells for identification and discrimination.     

High-pressure induced conformational and phase transformations of 1,2-dichloroethane probed by Raman spectroscopy

1,2-Dichloroethane (DCE) was loaded into diamond anvil cells and compressed up to 30 GPa at room temperature. Pressure-induced transformations were probed using Raman spectroscopy. At pressures below 0.6 GPa, fluid DCE exists in two conformations, gauche and trans in equilibrium, which is shifted to gauche on compression. DCE transforms to a solid phase with exclusive trans conformation upon further compression. All the characteristic Raman shifts remain constant in fluid phase and move to higher frequencies in the solid phase with increasing pressure. At about 4-5 GPa, DCE transforms from a possible disordered phase into a crystalline phase as evidenced by the observation of several lattice modes and peak narrowing. At 8-9 GPa, dramatic changes in Raman patterns of DCE were observed. The splitting of the C-C-Cl bending mode at 325 cm-1, together with the observation of inactive internal mode at 684 cm-1 as well as new lattice modes indicates another pressure-induced phase transformation. All Raman modes exhibit significant changes in pressure dependence at the transformation pressure. The new phase remains crystalline, but likely with a lower symmetry. The observed transformations are reversible in the entire pressure region upon decompression.     

Quantitative monitoring of yeast fermentation using Raman spectroscopy

Compared to traditional IR methods, Raman spectroscopy has the advantage of only minimal interference from water when measuring aqueous samples, which makes this method potentially useful for in situ monitoring of important industrial bioprocesses. This study demonstrates real-time monitoring of a Saccharomyces cerevisiae fermentation process using a Raman spectroscopy instrument equipped with a robust sapphire ball probe. A method was developed to correct the Raman signal for the attenuation caused by light scattering cell particulate, hence enabling quantification of reaction components and possibly measurement of yeast cell concentrations. Extinction of Raman intensities to more than 50 % during fermentation was normalized with approximated extinction expressions using Raman signal of water around 1,627 cm^?1 as internal standard to correct for the effect of scattering. Complicated standard multi-variant chemometric techniques, such as PLS, were avoided in the quantification model, as an attempt to keep the monitoring method as simple as possible and still get satisfactory estimations. Instead, estimations were made with a two-step approach, where initial scattering correction of attenuated signals was followed by linear regression. In situ quantification measurements of the fermentation resulted in root mean square errors of prediction (RMSEP) of 2.357, 1.611, and 0.633 g/L for glucose, ethanol, and yeast concentrations, respectively.     

Raman and surface Raman spectroscopy with ultraviolet excitation

We record the accurate and reliable Raman spectra of benzoic acid (BA), p-nitrobenzoic acid (PNBA) and o-nitrobenzoic (ONBA) in aqueous solution with ultraviolet excitation. And we find that the ultraviolet (UV) Raman spectrum of aqueous BA solution has one-to-one correspondence to that of BA solid whereas the others are less resemble to the solid counterparts. We also report surface Raman spectroscopy of them in silver colloid without any enhancement in UV region and call it surface-unenhanced Raman spectroscopy (SUERS) while the surface-enhanced Raman scattering (SERS) effects are perfect in near infrared or visible regions. It demonstrates the SERS effects are strongly dependent on the excitation wavelength. On the basis of the experiments, we discuss the mechanism of SERS excited in different regions.     

Probing history with Raman spectroscopy

This Tutorial Review shows how Raman spectroscopic and microscopic techniques are utilised for non-destructive characterisation of archaeological artefacts and provide novel information for art historians and hints at the use of ancient technologies for the production and treatment of materials and skeletal remains.     

Quantitative label-free RNA detection using surface-enhanced Raman spectroscopy

Surface-Enhanced Raman Spectroscopy (SERS) was performed to detect label-free RNA. We defined conditions which make it possible to probe the four bases of RNA, in single strands of polyadenosine (pA), polyuridine (pU), polycytosine (pC) and polyguanosine (pG). We therefore present below a quantitative analysis of mixtures of non-hybridized single strands, based on the deconvolution of the SERS mixture spectrum into the relative contributions of the SERS spectra of each constituent.